[FLASH-USERS] Compiling problem on SL6

[Seyit Hocuk]

Hi Chris,

Thanks for replying. No I hadn't solved the problem yet. I was thinking 
it is a linking problem and might be that an additional flag was 
required for linking in SL6 , although, I did not have any success yet. 
I never thought of glibc. I don't have static in FLASH link options (in 
Makefile.h), but I don't know how glibc it is built on my system.

"$ repoquery --list glibc-static" gives me this
/usr/lib/libBrokenLocale.a
/usr/lib/libanl.a
/usr/lib/libc.a
/usr/lib/libc_stubs.a
/usr/lib/libcrypt.a
/usr/lib/libdl.a
/usr/lib/libm.a
/usr/lib/libnsl.a
/usr/lib/libpthread.a
/usr/lib/libresolv.a
/usr/lib/librt.a
/usr/lib/libutil.a
/usr/lib64/libBrokenLocale.a
/usr/lib64/libanl.a
/usr/lib64/libc.a
/usr/lib64/libc_stubs.a
/usr/lib64/libcrypt.a
/usr/lib64/libdl.a
/usr/lib64/libm.a
/usr/lib64/libnsl.a
/usr/lib64/libpthread.a
/usr/lib64/libresolv.a
/usr/lib64/librt.a
/usr/lib64/libutil.a

while "$ repoquery --list glibc-static" returns me nothing on Cenos5 (I 
still have a machine with Centos5 where I can test things). Could it be 
that I use glibc-static unintentionally instead of the normal glibc? 
Perhaps I can set this in the Makefile.h.

On an another note, +noio option still fails and gives the same error. 
That is,
>
/net/ulubey/data/users/seyit/programmas/Libraries/lib64/mpich2-1.0.7/MPICH2/lib 
  -lmpich
> /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../lib64/crt1.o: In
function `_start':
> (.text+0x12): undefined reference to `__libc_csu_fini' ... etc


Kind regards,
Seyit

ps: Could the error possibly be due to the wrong elf-class? The first 
file that the error shows is "/usr/lib64/crt1.o". On my old system, I 
also had the 32-bit version of this file "/usr/lib/crt1.o". Were I 
somehow using the 32-bit version then? I wish there was a way to confirm 
this.



On 11/29/2011 12:17 AM, Christopher Daley wrote:
> Hi Seyit,
>
> Did you ever resolve this problem?
>
>
> These symbols exist in libpthread and libc.  Perhaps you are trying to
> link statically and have not yet installed a static glibc for you
> clean Scientific-Linux 6 installation:
>
> $ repoquery --list glibc-static
> /usr/lib64/libBrokenLocale.a
> /usr/lib64/libanl.a
> /usr/lib64/libc.a
> /usr/lib64/libc_stubs.a
> /usr/lib64/libcrypt.a
> /usr/lib64/libdl.a
> /usr/lib64/libm.a
> /usr/lib64/libnsl.a
> /usr/lib64/libpthread.a
> /usr/lib64/libresolv.a
> /usr/lib64/librt.a
> /usr/lib64/libutil.a
>
> If so, try installing the glibc-static package or remove the -static
> option from your FLASH link options.
>
>
> If the link still fails then you should test if it fails when you
> remove the FLASH I/O library dependence, i.e. setup FLASH with +noio.
>
> Chris
>
>
> On 11/18/2011 05:06 AM, Seyit Hocuk wrote:
>> Dear all,
>>
>> I have recently switched to Scientific Linux 6 (from CenOS 5), but now I
>> cannot compile my code anymore. Below is a snippet of the error. It
>> happens during the linking stage. Can anyone comment on this?
>>
>> I use my own fortran compiler (ifort 10.1.017)
>> I use my own mpich (2.1.0.7)
>> I use hdf5 version 1.8.1 (with api bindings for 1.6)
>> These libraries are unchanged from Centos5 to SL6.
>>
>> I use the systems default gcc, which has changed from C5 to SL6.
>>
>> I've tried to reinstall ifort and mpich, even tried to use intelcc
>> instead of gcc, but compiling still goes wrong. The problem lies surely
>> in one of these. Is it gcc, mpich, or hdf5?
>>
>> Kind regards,
>> Seyit
>>
>>
>>
>> ......tree.o umap.o user_coord_transfm.o ut_conversionInterface.o
>> ut_convertToArrayIndicies.o ut_convertToMemoryOffset.o ut_fndpos.o
>> ut_hunt.o ut_interpolationInterface.o ut_polint.o ut_quadraticInterpol.o
>> ut_sortInterface.o ut_sortOnProcs.o workspace.o
>> -L/net/ulubey/data/users/seyit/programmas/Libraries/lib64/hdf5-1.8.1/hdf5/lib
>>
>> -lhdf5 -lz -L
>> /net/ulubey/data/users/seyit/programmas/Libraries/lib64/mpich2-1.0.7/MPICH2/lib
>>
>> -lmpich
>>
>> /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../lib64/crt1.o: In
>> function `_start':
>> (.text+0x12): undefined reference to `__libc_csu_fini'
>> /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../lib64/crt1.o: In
>> function `_start':
>> (.text+0x19): undefined reference to `__libc_csu_init'
>> /net/ulubey/data/users/seyit/programmas/Libraries/lib64/mpich2-1.0.7/MPICH2/lib/libmpich.a(abort.o):
>>
>> In function `MPI_Abort':
>> abort.c:(.text+0x22a): undefined reference to `pthread_getspecific'
>> abort.c:(.text+0x25a): undefined reference to `pthread_getspecific'
>> abort.c:(.text+0x369): undefined reference to `pthread_setspecific'
>> abort.c:(.text+0x3ae): undefined reference to `pthread_setspecific'
>> /net/ulubey/data/users/seyit/programmas/Libraries/lib64/mpich2-1.0.7/MPICH2/lib/libmpich.a(initthread.o):
>>
>> In function `MPIR_Init_thread':
>> initthread.c:(.text+0x32e): undefined reference to `pthread_getspecific'
>> initthread.c:(.text+0x354): undefined reference to `pthread_setspecific'
>> /net/ulubey/data/users/seyit/programmas/Libraries/lib64/mpich2-1.0.7/MPICH2/lib/libmpich.a(initthread.o):
>>
>> In function `MPI_Init_thread':
>> initthread.c:(.text+0x3fa): undefined reference to `pthread_key_create'
>> initthread.c:(.text+0x4d9): undefined reference to `pthread_key_delete'
>> initthread.c:(.text+0x517): undefined reference to `pthread_getspecific'
>> initthread.c:(.text+0x543): undefined reference to `pthread_setspecific'
>> initthread.c:(.text+0x567): undefined reference to `pthread_getspecific'
>> initthread.c:(.text+0x593): undefined reference to `pthread_setspecific'
>> initthread.c:(.text+0x5bf): undefined reference to `pthread_getspecific'
>> initthread.c:(.text+0x5dc): undefined reference to `pthread_setspecific'
>> initthread.c:(.text+0x5ec): undefined reference to `pthread_getspecific'
>> initthread.c:(.text+0x618): undefined reference to `pthread_setspecific'
>> initthread.c:(.text+0x63d): undefined reference to `pthread_setspecific
>> .... etc. etc.
>